It's not just you. I have this behavior 80% of the time I start Sabayon 4.0. The oddest part is that if I restart X (Ctrl-Alt-Backspace) everything works as it should.

Strictly speaking, any Alt+ combo seems to be grabbing a default Ctrl key as well, sticking us in other terminals. The Win key is grabbing such as well. My culprit is Alt+F2, since I use that everytime I launch an app.

Even odder, the proper command does get passed to X - when you switch back to the GUI, the dialog (be it the Run dialog, or the Kmenu) is present and waiting.

This preserves the ability to switch TTY consoles while in them, using Ctrl Alt, while removing the Alt functionality that was conflicting, and the Winkey behavior as well. And the Alt+left and Alt+right behavior.